Package evaluation of CHMMAIRRa on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T08:06:15.685


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 5.23s


################################################################################
# Installation
#

Installing CHMMAIRRa...
   Resolving package versions...
   Installed CHMMAIRRa ─ v0.0.2
    Updating `~/.julia/environments/v1.10/Project.toml`
  [d8677c85] + CHMMAIRRa v0.0.2
    Updating `~/.julia/environments/v1.10/Manifest.toml`
  [c7e460c6] + ArgParse v1.2.0
  [d8677c85] + CHMMAIRRa v0.0.2
  [4c20a592] + CHMMera v0.1.2
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.16.0
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.20
  [e2d170a0] + DataValueInterfaces v1.0.0
  [48062228] + FilePathsBase v0.9.23
  [842dd82b] + InlineStrings v1.4.3
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [e1d29d7a] + Missings v1.2.0
  [bac558e1] + OrderedCollections v1.8.0
  [69de0a69] + Parsers v2.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [189a3867] + Reexport v1.2.2
  [91c51154] + SentinelArrays v1.4.8
  [a2af1166] + SortingAlgorithms v1.2.1
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [b718987f] + TextWrap v1.0.2
  [3bb67fe8] + TranscodingStreams v0.11.3
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [de0858da] + Printf
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0

Installation completed after 7.96s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 18.82s


################################################################################
# Testing
#

     Testing CHMMAIRRa
      Status `/tmp/jl_KLpFqm/Project.toml`
  [c7e460c6] ArgParse v1.2.0
  [d8677c85] CHMMAIRRa v0.0.2
  [4c20a592] CHMMera v0.1.2
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [a93c6f00] DataFrames v1.7.0
  [9a3f8284] Random
  [8dfed614] Test
      Status `/tmp/jl_KLpFqm/Manifest.toml`
  [c7e460c6] ArgParse v1.2.0
  [d8677c85] CHMMAIRRa v0.0.2
  [4c20a592] CHMMera v0.1.2
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.16.0
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.7.0
  [864edb3b] DataStructures v0.18.20
  [e2d170a0] DataValueInterfaces v1.0.0
  [48062228] FilePathsBase v0.9.23
  [842dd82b] InlineStrings v1.4.3
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [b964fa9f] LaTeXStrings v1.4.0
  [e1d29d7a] Missings v1.2.0
  [bac558e1] OrderedCollections v1.8.0
  [69de0a69] Parsers v2.8.1
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
  [189a3867] Reexport v1.2.2
  [91c51154] SentinelArrays v1.4.8
  [a2af1166] SortingAlgorithms v1.2.1
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [b718987f] TextWrap v1.0.2
  [3bb67fe8] TranscodingStreams v0.11.3
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [de0858da] Printf
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] OpenBLAS_jll v0.3.23+4
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
     Testing Running tests...
utils.jl: Error During Test at /home/pkgeval/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:22
  Got exception outside of a @test
  Could not find mafft executable. Please ensure mafft is installed and in your PATH, or provide the path using --mafft
  Stacktrace:
    [1] error(s::String)
      @ Base ./error.jl:35
    [2] #mafft_wrapper#23
      @ ~/.julia/packages/CHMMAIRRa/ahDZ6/src/utils.jl:103 [inlined]
    [3] mafft_wrapper(seqs::Vector{String}, seqnames::Vector{String})
      @ CHMMAIRRa ~/.julia/packages/CHMMAIRRa/ahDZ6/src/utils.jl:94
    [4] macro expansion
      @ ~/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:71 [inlined]
    [5] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
    [6] macro expansion
      @ ~/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:24 [inlined]
    [7] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
    [8] top-level scope
      @ ~/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:22
    [9] include(fname::String)
      @ Base.MainInclude ./client.jl:494
   [10] top-level scope
      @ none:6
   [11] eval
      @ ./boot.jl:385 [inlined]
   [12] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:296
   [13] _start()
      @ Base ./client.jl:557
Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment
Threading alignment
Running forward algorithm to get chimerism probabilities
Running viterbi to get chimeric paths
Number of chimeric sequences: 1 (50.0%)
Counting chimeric segments
Finding chimeric alignments
Done.
------------------------------ Processing chunk 1 ------------------------------
Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment
Threading alignment
Running forward algorithm to get chimerism probabilities
Running viterbi to get chimeric paths
Number of chimeric sequences: 1 (100.0%)
Finding chimeric alignments
------------------------------ Processing chunk 2 ------------------------------
Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment
Threading alignment
Running forward algorithm to get chimerism probabilities
Running viterbi to get chimeric paths
Number of chimeric sequences: 0 (0.0%)
Finding chimeric alignments
------------------------------ Processing chunk 3 ------------------------------
Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment
Threading alignment
Running forward algorithm to get chimerism probabilities
Running viterbi to get chimeric paths
Number of chimeric sequences: false (NaN%)
Finding chimeric alignments
Done.
Test Summary:  | Pass  Error  Total     Time
CHMMAIRRa.jl   |   39      1     40  1m49.0s
  utils.jl     |   17      1     18    46.0s
  CHMMAIRRa.jl |   22            22  1m02.9s
ERROR: LoadError: Some tests did not pass: 39 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:21

Testing failed after 120.36s

ERROR: LoadError: Package CHMMAIRRa errored during testing
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
   @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2034
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined]
 [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::Base.PipeEndpoint})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
 [8] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:219
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 160.43s: package tests unexpectedly errored